1. They genuinely didn't know about Let's Encrypt
2. Learning some new stuff to get a free cert didn't seem worth it because they're not paying anyway (at corps this is often because they have a bulk deal, or there will just be a Purchase Order so it's not their personal credit card bill, for crooks it's probably someone else's money anyway)
3. Some minor technical inconvenience made doing the ACME proof of control validations tricky. For example their DNS provider doesn't implement a sane API for changing TXT records.
There are other examples, the Nintendo Wii U, Internet Explorer on old enough XP (but really old XP can't grok modern TLS anyway and so you're screwed) but we're quickly talking about the minority of a minority.
I'm sure the perception was there though.
"Minority of a minority", maybe, but I still got around five tweets about it when it happened; more than most other changes I make.
https://www.reddit.com/r/pokemonshowdown/comments/7eix1o/pok...
The problem wasn't just because of the HTTPS cert, but also because it didn't support WebSocket on port 8000.
As usual in DNS this works fine in the Free implementation your OS vendor included, shame about all the expensive proprietary choices that get this wrong for every single new record type.
It's a pity it isn't just a TXT record.
Even if they are paying, the ROI on spending even a single day on learning new stuff is a long, long time if you're just buying a DV cert.
A security team reviewing that baways.com site would definitely make note of the fact that it was using letsencrypt.
Letsencrypt certs are widely used by malicious actors. Thus one not being used is noteworthy and why RiskIQ made note of it.
If someone who's downvoting me would like to show some examples of major websites from Fortune 100s or large international firms (like BA) using letsencrypt certs to collect payment info, then by all means, please do.